Ctenoides ales genome assembly

<b>Title:</b> Chromosome-level genome assembly of the disco clam, <i>Ctenoides ales</i>, a first for the bivalve order Limida<b>Abstract: </b>The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present the first limid genome assembly, the disco clam, <i>Ctenoides ales</i>, which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-C^TM proximity-ligation sequencing. The final assembly is ~2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and report a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a completely annotated mitochondrial genome, also a first for Limida. The ~20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The <i>C. ales</i> nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, <i>C. ales</i> lacks duplication of the rhabdomeric G_q-protein coupled opsin that is typically used for invertebrate vision. In fact, <i>C. ales</i> has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, will be valuable resources for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.<br><b>Items in dataset</b>Cale_mtGenome.fasta - Ctenoides ales mitochondrial genome assemblyCale_mtGenome_annotation.bed - Ctenoides ales mitochondrial genome annotationCollapsedCalesMikado.proteins.fasta.gz - proteins from genome annotation of Ctenoides ales genomeCollapsedCalesMikado.transcripts.fasta.gz - transcripts from genome annotation of Ctenoides ales genomeSortedFunctionalAnnotationCales.gff3.gz - annotation files of Ctenoides ales genome assemblySoftmaskedCalesGenomeCleanScaffolds.fasta.gz - Ctenoides ales genome assembly fileOpsin_seqs.aa.fa - opsin sequences (amino acid) from Ctenoides ales and other pteriomorphian bivalve speciesOpsin_seqs.aln.aa.fa - aligned opsin sequences (amino acid) from Ctenoides ales and other pteriomorphian bivalve speciesOpsin_treefile.nwk - ML phylogenetic tree of pteriomorphian opsins and outgroup sequences (newick format)Opsin_treefile.nxs - ML phylogenetic tree of pteriomorphian opsins and outgroup sequences (nexus format, rooted)Opsin_IQTREE.log.txt - log file for IQ-TREE2 analysis of opsin sequencespartition_models.nex.treefile.rooted.nxs - ML species tree of pteriomorphian bivavles and outgroups based on partitioned analysis of 1,156 single copy orthologs (nexus format, rooted)IQtree2_partition_bivalve.nwk - ML species tree of pteriomorphian bivavles and outgroups based on partitioned analysis of 1,156 single copy orthologs (newick format)<br>

<b>Title:</b> 双壳纲狐蛤目（Limida）首份染色体水平基因组组装：闪光碟贝<i>Ctenoides ales</i>
<b>Abstract: </b>翼形亚纲（Pteriomorphia）双壳类包含扇贝、牡蛎、贻贝、魁蚶等具有重要经济价值的类群，其生态、形态及行为多样性极高。该类群演化出五种形态截然不同的眼型，使其成为探究新性状演化分子基础的理想研究体系。在翼形亚纲双壳类中，狐蛤目（Limida）是唯一缺乏基因组资源的类群，极大制约了与眼及光转导相关的系统基因组学研究开展。本研究成功构建了首个狐蛤目基因组组装序列——闪光碟贝<i>Ctenoides ales</i>，该物种具备内陷型眼、超长触手以及闪光行为等特征。本基因组组装采用PacBio长读长测序与Dovetail Omni-C^TM邻近连接测序技术构建。最终组装的基因组大小约为2.3 Gb，总序列长度的99%以上被锚定至18条假染色体支架。本研究共注释得到41064个蛋白质编码基因，基于metazoa_obd10数据库的BUSCO评估显示基因组完整性达91.9%。此外，本研究还报道了狐蛤目首个完成全注释的线粒体基因组。该线粒体基因组全长约20 Kb，包含12个蛋白质编码基因、22个tRNA基因、2个rRNA基因，以及一段长1589 bp的携带复制起点的重复序列。<i>C. ales</i>的核基因组大小显著大于其他翼形亚纲基因组，该差异主要由转座因子（transposable element）序列扩张所致。我们对基因组中启动光转导的视蛋白（opsins）信号蛋白进行了系统检索，发现与亲缘关系最近的带眼类群扇贝不同，<i>C. ales</i>缺乏通常用于无脊椎动物视觉的杆体细胞型G_q蛋白偶联视蛋白的复制事件。事实上，相较于其他翼形亚纲类群（这些类群均具有新近发现的异视蛋白（xenopsins）的独特扩张），<i>C. ales</i>的视蛋白数量异常稀少。这份染色体水平基因组组装连同线粒体基因组，将为双壳类，尤其是研究不足但极具魅力的狐蛤目类群的比较基因组学与系统发育学研究提供宝贵资源。
<b>Items in dataset</b>
Cale_mtGenome.fasta - <i>Ctenoides ales</i>线粒体基因组组装文件
Cale_mtGenome_annotation.bed - <i>Ctenoides ales</i>线粒体基因组注释文件
CollapsedCalesMikado.proteins.fasta.gz - <i>Ctenoides ales</i>基因组注释所得蛋白质序列文件
CollapsedCalesMikado.transcripts.fasta.gz - <i>Ctenoides ales</i>基因组注释所得转录本序列文件
SortedFunctionalAnnotationCales.gff3.gz - <i>Ctenoides ales</i>基因组组装功能注释文件
SoftmaskedCalesGenomeCleanScaffolds.fasta.gz - <i>Ctenoides ales</i>软屏蔽版基因组组装文件
Opsin_seqs.aa.fa - <i>Ctenoides ales</i>及其他翼形亚纲双壳类的视蛋白氨基酸序列文件
Opsin_seqs.aln.aa.fa - <i>Ctenoides ales</i>及其他翼形亚纲双壳类的比对后视蛋白氨基酸序列文件
Opsin_treefile.nwk - 翼形亚纲视蛋白及外类群序列的最大似然法（ML）系统发育树文件（Newick格式）
Opsin_treefile.nxs - 翼形亚纲视蛋白及外类群序列的最大似然法系统发育树文件（Nexus格式，已根化）
Opsin_IQTREE.log.txt - 视蛋白序列IQ-TREE2分析日志文件
partition_models.nex.treefile.rooted.nxs - 基于1156个单拷贝直系同源基因分区分析得到的翼形亚纲双壳类及外类群的最大似然法物种树文件（Nexus格式，已根化）
IQtree2_partition_bivalve.nwk - 基于1156个单拷贝直系同源基因分区分析得到的翼形亚纲双壳类及外类群的最大似然法物种树文件（Newick格式）